Last updated: 2020-06-08

Checks: 5 2

Knit directory: ~/Research-Local/2019-rnaseq/TCGA-Nigerian-RNAseq/

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#Translation from HTSeq raw counts -> Count Matrix I have 84 TCGA patients with whole-genome sequencing data and RNAseq data as well as 95 Nigerian patients with RNA-seq data. Raw counts were initially processed using HTSeq, so HTSeq data is being formatted for use with DESeq2 and limma-voom.

                   sampleConditionPAM50
sampleConditionrace Basal Her2 LumA LumB Normal PAM_other
         Nigerian      29   24   14   16      6         6
         TCGA_black    23    0    4    4      0         0
         TCGA_other     0    0    0    0      0        14
         TCGA_white    17    5    8    9      0         0

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#Quantile normalization Please refer to: https://parajago.github.io/TCGA-Nigerian-RNAseq/NigerianTCGArawcountsDeSeq2-pc2.html regarding comparison between the Nigerian and TCGA data sets and why quantile normalization under the limma-voom approach was chosen for primary differential expression analysis.

##Data visualization

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#Differential expression setup

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##DE: Nigerian/TCGA White - Basal

[1] 5172   46

       TCGA_white.Basal - Nigerian.Basal
Down                                 492
NotSig                              4562
Up                                   118

Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.

##DE: Nigerian/TCGA Black - Basal

[1] 5305   52

       TCGA_black.Basal - Nigerian.Basal
Down                                 398
NotSig                              4786
Up                                   121

Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.

##DE: Nigerian/TCGA White - HER2 (no TCGA Black HER2+ patients)

[1] 4652   29

       TCGA_white.Her2 - Nigerian.Her2
Down                               620
NotSig                            3897
Up                                 135

Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.

##DE: Nigerian/TCGA White - LumA

[1] 4211   22

       TCGA_white.LumA - Nigerian.LumA
Down                               367
NotSig                            3780
Up                                  64

Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.

##DE: Nigerian/TCGA Black - LumA

[1] 4056   18

       TCGA_black.LumA - Nigerian.LumA
Down                               370
NotSig                            3634
Up                                  52

Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.

##DE: Nigerian/TCGA White - LumB

[1] 4272   25

       TCGA_white.LumB - Nigerian.LumB
Down                               285
NotSig                            3933
Up                                  54

Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.

##DE: Nigerian/TCGA Black - LumB

[1] 4081   20

       TCGA_black.LumB - Nigerian.LumB
Down                               333
NotSig                            3630
Up                                 118

Warning: The above code chunk cached its results, but it won’t be re-run if previous chunks it depends on are updated. If you need to use caching, it is highly recommended to also set knitr::opts_chunk$set(autodep = TRUE) at the top of the file (in a chunk that is not cached). Alternatively, you can customize the option dependson for each individual chunk that is cached. Using either autodep or dependson will remove this warning. See the knitr cache options for more details.


sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] msigdbr_7.1.1               fgsea_1.10.0               
 [3] Rcpp_1.0.1                  AnnotationHub_2.16.1       
 [5] BiocFileCache_1.8.0         dbplyr_1.4.2               
 [7] Glimma_1.12.0               RColorBrewer_1.1-2         
 [9] preprocessCore_1.46.0       ashr_2.2-32                
[11] ggfortify_0.4.7             calibrate_1.7.2            
[13] MASS_7.3-51.5               sva_3.32.1                 
[15] mgcv_1.8-31                 nlme_3.1-144               
[17] EnsDb.Hsapiens.v75_2.99.0   ensembldb_2.8.0            
[19] AnnotationFilter_1.8.0      GenomicFeatures_1.36.4     
[21] hexbin_1.27.3               stringi_1.4.3              
[23] dplyr_0.8.3                 affy_1.62.0                
[25] checkmate_1.9.3             pathview_1.24.0            
[27] org.Hs.eg.db_3.8.2          AnnotationDbi_1.46.0       
[29] clusterProfiler_3.12.0      pheatmap_1.0.12            
[31] genefilter_1.66.0           vsn_3.52.0                 
[33] RUVSeq_1.18.0               EDASeq_2.18.0              
[35] ShortRead_1.42.0            GenomicAlignments_1.20.0   
[37] Rsamtools_2.0.0             Biostrings_2.52.0          
[39] XVector_0.24.0              DESeq2_1.24.0              
[41] SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
[43] BiocParallel_1.18.0         matrixStats_0.54.0         
[45] Biobase_2.44.0              GenomicRanges_1.36.0       
[47] GenomeInfoDb_1.20.0         IRanges_2.18.1             
[49] S4Vectors_0.22.0            BiocGenerics_0.30.0        
[51] edgeR_3.26.4                limma_3.40.2               
[53] ggbiplot_0.55               scales_1.0.0               
[55] plyr_1.8.5                  ggplot2_3.2.1              
[57] gplots_3.0.3               

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1                rtracklayer_1.44.0           
  [3] R.methodsS3_1.7.1             tidyr_1.0.0                  
  [5] acepack_1.4.1                 bit64_0.9-7                  
  [7] knitr_1.28                    aroma.light_3.14.0           
  [9] R.utils_2.8.0                 data.table_1.12.8            
 [11] rpart_4.1-15                  hwriter_1.3.2                
 [13] KEGGREST_1.24.0               RCurl_1.95-4.12              
 [15] doParallel_1.0.14             cowplot_0.9.4                
 [17] RSQLite_2.1.1                 europepmc_0.3                
 [19] bit_1.1-14                    enrichplot_1.4.0             
 [21] xml2_1.3.2                    httpuv_1.5.2                 
 [23] assertthat_0.2.1              viridis_0.5.1                
 [25] xfun_0.7                      hms_0.5.2                    
 [27] evaluate_0.14                 promises_1.0.1               
 [29] progress_1.2.2                caTools_1.17.1.2             
 [31] Rgraphviz_2.28.0              igraph_1.2.4.1               
 [33] DBI_1.0.0                     geneplotter_1.62.0           
 [35] htmlwidgets_1.3               purrr_0.3.3                  
 [37] backports_1.1.4               annotate_1.62.0              
 [39] biomaRt_2.40.0                vctrs_0.2.0                  
 [41] withr_2.1.2                   ggforce_0.2.2                
 [43] triebeard_0.3.0               prettyunits_1.0.2            
 [45] cluster_2.1.0                 DOSE_3.10.1                  
 [47] lazyeval_0.2.2                crayon_1.3.4                 
 [49] labeling_0.3                  pkgconfig_2.0.2              
 [51] tweenr_1.0.1                  ProtGenerics_1.16.0          
 [53] nnet_7.3-12                   rlang_0.4.5                  
 [55] lifecycle_0.1.0               affyio_1.54.0                
 [57] rprojroot_1.3-2               polyclip_1.10-0              
 [59] graph_1.62.0                  Matrix_1.2-18                
 [61] urltools_1.7.3                base64enc_0.1-3              
 [63] ggridges_0.5.1                png_0.1-7                    
 [65] viridisLite_0.3.0             bitops_1.0-6                 
 [67] R.oo_1.22.0                   KernSmooth_2.23-16           
 [69] blob_1.1.1                    workflowr_1.4.0              
 [71] mixsqp_0.1-97                 stringr_1.4.0                
 [73] SQUAREM_2017.10-1             qvalue_2.16.0                
 [75] gridGraphics_0.4-1            memoise_1.1.0                
 [77] magrittr_1.5                  gdata_2.18.0                 
 [79] zlibbioc_1.30.0               compiler_3.6.3               
 [81] KEGGgraph_1.44.0              htmlTable_1.13.1             
 [83] Formula_1.2-3                 tidyselect_0.2.5             
 [85] yaml_2.2.0                    GOSemSim_2.10.0              
 [87] locfit_1.5-9.1                latticeExtra_0.6-28          
 [89] ggrepel_0.8.1                 fastmatch_1.1-0              
 [91] tools_3.6.3                   rstudioapi_0.11              
 [93] foreach_1.4.4                 foreign_0.8-75               
 [95] git2r_0.26.1                  gridExtra_2.3                
 [97] farver_1.1.0                  ggraph_1.0.2                 
 [99] digest_0.6.25                 rvcheck_0.1.3                
[101] BiocManager_1.30.10           shiny_1.3.2                  
[103] pscl_1.5.2                    later_0.8.0                  
[105] httr_1.4.1                    colorspace_1.4-1             
[107] XML_3.98-1.20                 fs_1.3.1                     
[109] truncnorm_1.0-8               splines_3.6.3                
[111] ggplotify_0.0.3               xtable_1.8-4                 
[113] jsonlite_1.6.1                UpSetR_1.4.0                 
[115] zeallot_0.1.0                 R6_2.4.0                     
[117] Hmisc_4.2-0                   pillar_1.4.2                 
[119] htmltools_0.3.6               mime_0.7                     
[121] glue_1.4.0                    DESeq_1.36.0                 
[123] interactiveDisplayBase_1.22.0 codetools_0.2-16             
[125] lattice_0.20-38               tibble_2.1.3                 
[127] curl_4.3                      gtools_3.8.1                 
[129] GO.db_3.8.2                   survival_3.1-8               
[131] rmarkdown_2.1                 munsell_0.5.0                
[133] DO.db_2.9                     GenomeInfoDbData_1.2.1       
[135] iterators_1.0.10              reshape2_1.4.3               
[137] gtable_0.3.0